When the Darkness Comes
by mariteri
Summary: When S.H.I.E.L.D. falls, Hermione and Phil must deal with not only with that but with their own marriage as well. Rated T for implied violence.
**Disclaimer—I do not own Harry Potter, Agents of S.H.I.E.L.D. or any of the characters therein. Nor do I earn any moneys from the posting of this fanfiction.**

 **Hey! Just a one-shot here for Hermione and Phil! Enjoy.**

 **Please read and review.**

 **…**

 **When the Darkness Comes**

The world seemed to collapse causing the chaos that enveloped Hermione's life. S.H.I.E.L.D.'s implosion was only the beginning. It had started out as a normal day—well, if you considered being held at gun point and being told that she was to join H.Y.D.R.A. or die normal that is. It wasn't helped that it had been by her own assistant at that. The poor woman never knew what hit her. Nor, for that matter, did anyone else that crossed her path attempting to pull her in, control, or even kill her.

Being left with no other option, Hermione wiped the computers and proceeded to fry what was left with her magic. She took out the surveillance and casually was able to knock out every individual that crossed her path. And as all of them seemed to pull weapons on her, it was safe to assume that they weren't on her side of things. One of the times, and she didn't even understand how this could have happened, when she magically took out one of the guards holding their automatic weapons on her, all the other twelve around her jolted and dropped to the ground dead. Terror along with the drive to survive had her all but running as she was finishing up what she had been doing. Hermione was cleaning out and frying the computer systems, when her phone started to ring.

She answered the phone with, "Can't speak now, Phil."

"Are you safe?"

Gunfire rang out, having her ducking under the desk she was at and saying, "No." Several other shots rang out. "Hold on…"

"Hermione!" he yelled, even as she set down the phone to deal with the people firing on her.

The two people who had been firing on her were still falling to the ground, as she took up the phone again. "Like I said, I can't speak right now." Swallowing thickly, as she saw more people in H.Y.D.R.A. uniforms running towards her. "Phil, I love you."

"Hermione?"

"I love you so much," she breathed, even as he was screaming at her.

"Hermione!" She hung up the phone and proceeded to bring hell to the party.

She took the fight to the guards, none of whom knew how to fight against magic. Hermione fought coolly and efficiently, making her way straight out of the building. But even so it was a limping, bleeding Hermione who walked out of that place. As soon as she was far enough away, she hit the detonator in her hand and the building was blowing up behind her. It was with tears dripping down her face, as she vanished out of sight.

…

Phil walked around the facility with May, Jemma, and Tripp. The terror that had settled around his heart, grew with each and every one of the bodies they had found. On more than one occasion, Phil rushed over to the white coated women to look at their faces. There was relief as well as fear of what was to come.

"Who are you looking for?" Tripp asked him.

"My wife," he muttered.

"Wait!" Jemma stopped him. "Who is your wife?"

Taking a deep breath, he said, "Dr. Hermione Granger."

Jemma's eyes went wide. "Thee Dr. Granger?"

Skye came running over, saying, "The firemen say there's no way we can get upstairs. That the structure wouldn't be able to take the stress of anyone trying to get up there."

"Are there…" Coulson swallowed thickly. "Are there bodies up there?"

"A bunch," she answered before she noticed Jemma trying to tell her with hand motions not to say anything. "What's going on?"

Coulson's phone rang and he answered it, "What?"

There was a pause followed by, "Now I know something very big happened, but is that any reason to be rude, I ask you?"

"Where's Hermione?!" he snapped. "Is she with you, Fred? Is she okay?"

"Give me the bloody phone, you wanker!" The voice Phil heard in the background had him all but slumping in relief. There was a yelp followed by, "Phil?"

"I'm here, sweetheart," he said quietly. "Where are you?"

"The old house," she told him quietly. "Where can we meet up?"

He thought it over, saying, "Hold on." Looking over to May, he asked, "ETA to the UK?"

She thought it over. "Approximately four hours."

He nodded to this and got back on the line. "We can meet up at Mr. and Mrs. W's house in about five hours. I'll see you at the strip."

"Will do," she breathed. "Phil?"

"What?" he asked.

"We need to have a talk."

"I know," he said, sounding tired. "I know."

…

Hermione and Phil practically flew into each other's arms the moment they were within feet of each other. He combed her hair out of her face, kissing it between checking her for injuries.

"You're okay?" he asked finally.

She nodded, as she checked him over as well. "What the hell happened? How did H.Y.D.R.A. infiltrate S.H.I.E.L.D.?"

"I'll tell you everything in a few minutes, but we have someone with us that needs healing."

She nodded to this, as looked over to Harry.

"I'll get your bag," he assured her, as she went into the plane.

It was after a few steps that Phil saw that she was limping. Scooping her up off of her feet, he muttered, "You should have told me that you were hurt."

"I have a wrap on it," she assured him. "It'll be as right as rain in a couple more hours."

"Promise?" he asked in a low voice.

"I promise," she replied, kissing his ear.

Once they were in the med-bay, Phil set her onto her feet and she got to work on Fitz. Minutes later Harry was standing next to her with her bag in hand. She let out a long sigh, looking over to her friend.

"Floo Padma," she told him. "I'm going to need more help than you can give me."

Harry nodded and went off to do just that. She turned to look at her husband, saying, "Even with the tools that are at my disposal there's only going to be so much I can do for him."

He nodded, saying, "I understand."

They were silent a moment before flicking a look over to his team watching them from the window. Looking back over to Phil, she asked, "You haven't been writing to me." Clearing her throat, she added, "You promised."

"I know," he breathed. "This isn't the time or the place."

She was silent a moment before saying, "If you want it over…"

"No," he cut her off. "I don't." He went over to her, pulling her into his arms as he made her look him in the eyes. "I thought…I thought you'd…"

She cupped his face. "I love you, Phil Coulson. I have for a long time now and it isn't going to stop over the silly measures you have taken that you think will keep me safe."

"They weren't silly," he muttered.

"Phil, you saw the medical research facility?" He nodded slowly. "It didn't get that way without help."

His eyes went wide. "You?"

Nodded slowly, she murmured, "Me." Sighing heavily, a confused look came over her. "But I don't understand…some of them just dropped. I never touched them. It was like someone cut their strings."

He pulled her closer, rubbing her back. "It was the Clairvoyant's work."

"A clairvoyant? Really?" She rolled her eyes. "Please for the love of whatever creator there may be tell me that there's no prophecy!"

A small smile twisted his lips. "None that I know of." But then it faltered as he added, "It was Garrett."

She studied him a moment before saying, "I'm sorry for the loss of your friend."

"I doubt that he ever was my friend. He was H.Y.D.R.A., Hermione."

Hermione pursed her lips, muttering, "I wish that was coming as a shock."

He studied her a moment. "What do you mean?"

"He kept pushing for access to the medical division—something that he didn't have any reason to be given access to," she said quietly. "He had people posing as interns trying to get into places that they, again, had no reason to be let into. I tried to pass along that information, but I don't know if it got passed to Fury or Hill."

Phil rolled his eyes. "That makes sense."

"So is Garrett dead?" she asked quietly.

He nodded grimly.

Her arms went around him tightly, resting her head against his chest. "I'm so sorry, luv."

"I know," he said, kissing her temple.

They stood there for a time, holding each other before she said, "I'm not built to live completely alone."

He shivered at her words. "I'm not either."

"I agreed to this arrangement because I thought it would have you being the happiest," she whispered, pulling back slightly to look into his blue eyes. "But you aren't sleeping any more than I am, are you?"

He shook his head reluctantly.

"I want to join you on the bus," she told him. "And before you say it, let me remind you that I'm the head of nothing anymore, given the fact that S.H.I.E.L.D. is currently in shambles."

Swallowing thickly, he said, "I was made director."

Smiling she said, "Congratulations."

Blushing, he replied, "Thank you." But he cleared his throat and told her, "I have a doctor on board already."

The silence between them was heavy for a moment before she asked, "Can you at least tell me why you're pushing me away?"

He looked to her sharply, but said nothing.

"We took magical vows, Phil. There's no such thing as divorce in the magical world," she said, her voice sounding oddly detached. "I've always put you first. I see now that this may have been a mistake." Absent tears dripped down her face, as she pulled away from him.

"Please don't cry," he breathed, feeling his heart breaking at the sight of his strong wife's tear stained face.

"You're pushing me away!" She yelled at him. "What would you have me do, Philip?!"

"You'd be safer…"

"Bullocks to that!" she raged, just as Padma and Harry entered the medical bay. "I don't know what is in that head of yours passing for logic, but allow me to be the first to tell you that it's extremely faulty. Now if you will please excuse us, Padma and I need to work on our patient."

Once they were outside of the medical bay, Harry turned to Phil and snarled, "I swear to whatever god you pay mind to that I will break you into pieces if you hurt her any more than you have, Coulson." With those words, he turned to watch the healing being done in the other room.

"She safer being away from me," Phil said quietly.

Harry looked to him sharply. "Really?" He leaned closer to the older man, snarling, "If that was the case, you would never have married Hermione in the first place." He stepped away from him and went back to watching the witches at work.

…

It was an hour and a half later that Padma and Hermione walked out of the medical bay. Both were looking tired, as the joined the group in the other room.

"He's out of the coma," Hermione said, her voice devoid of emotion. "He has some minor brain damage that couldn't be reversed, but given time it can possibly heal on its own."

Padma nodded by way of saying goodbye and soon was on her way. Harry tried to get Hermione to go over to the Burrow.

"Leave me be," his friend said quietly. "I need to speak to my husband."

Phil and Hermione went over to his office. She went over and sat down across from him. He sat on the edge of his desk, watching her intently.

"You deserve better than what I've given you," he said quietly. "I love you. I think I always have from the first moment I saw that you never locked doors." He kneeled down next to her, taking her hands with his own. He rubbed her knuckles slowly. "But as much as I want to say that it's about your protection, we both know it's a lie."

She swallowed thickly. "We've worked damn hard to keep work as work and personal as personal. But we can't do it anymore, Phil."

He nodded. "I know you're right." He reached out to her and combed her hair out of her face. "I can't ask you to wait, but I can't ask you to stay on the Bus with me either."

"Why not?" she asked him, her eyes pleading with him. "We've given our life over to the job for so long. Is it too much to ask to have a slice of life that's our own?"

He pulled her closer to himself, kissing her mouth hungrily. "No, it isn't." He picked her up, stood up, turned around and sat down in the chair with her in his lap. Rubbing her hip, his said in a low voice, "You're coming with us."

Sighing she rested her forehead against his. Kissing his lips lightly, she sighed, "It's about time."

"But what will your job be?" he asked her.

"Teach Jemma, help with Fitz, be May's drinking partner, learn computers from Skye and listen to my husband even as I'm attempting to make sure that he sleeps sometime this century…"

Slapping her rear playfully, he was smiling as she giggled. "But will it be enough?" he asked her.

"I don't know," she answered seriously. "We won't know until we go through it. I will say this much, we're more than likely going to have to work at our marriage just as much now as we always have."

He caressed her face, telling her, "Our marriage has been the best job I've ever had."

Smiling she said, "Me too."

 **The End**

 **…**

 **So there you go! I hope that you all liked it. Thanks for reading and I hope that you are having a wonderful day!**


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